Flying Lessons
by MsRaven
Summary: What if Dr. Weir had the same ability to control Ancient Technology as Sheppard? WeirSheppard mostly friendship. Rated for some language and content in later chapters.
1. Revelations

**Flying Lessons**

**Summary:** What if Dr. Weir had the same ability to control Ancient Technology as Sheppard? Weir/Sheppard mostly friendship.

**Spoilers: **None really, but up to Suspicion to be safe.

**Disclaimers:** Stargate Atlantis and its characters do not belong to me.

**Author's Note:** This is part of what I'm starting to consider my Conversations Universe. You'll probably need to read Conversations and Ends and Means before reading this one. This is mostly a development of Weir and Sheppard's friendship, but it does have shippy undertones like in my other stories. If you don't agree with that pairing, you probably shouldn't read this. If you do choose to read this, I hope you enjoy it.

"Dr. Weir, please come to the chair room." Dr. Rodney McKay's voice is heard over the main communications system. Another voice, with a distinctive Scottish accent, is heard in the background, but what he's saying can't be made out. "Uh...Major Sheppard, you too."

Dr. Elizabeth Weir and Major John Sheppard meet each other just outside the "chair room". It is aptly named because it holds two command chairs like the one found in Antarctica. They have made several unsuccessful attempts to activate a weapon similar to what is on the puddle jumpers and what saved Earth from the Apophis attack. McKay has come to the conclusion that it will take two people who, not only have the Ancient gene, but have an upper level control of Ancient devices. Since there are no other members of Atlantis that can match Sheppard's uncanny ability to control all Ancient technology, they still lack a way to protect Atlantis from a direct attack by the Wraith.

"What have they done now?" Elizabeth asks John.

"We probably don't want to know."

The two walk into the room to find McKay and Dr. Carson Beckett standing over a computer console. They seem to be in the middle of an argument, which is nothing new.

"Is there something you wanted Rodney?" Weir sounds a little impatient. John knows that she hasn't gotten much sleep in the past few nights. The emergencies with the desalinization tanks and then the ventilation system have taken their toll. He should probably make sure they get this over with quickly so he can make her get some sleep.

"Ah. Dr. Weir, Major Sheppard! Thanks for coming so quickly. We were hoping you could help us out with a little experiment."

John and Elizabeth both roll their eyes. McKay's eyes are gleaming excitedly, so this can't be good.

"Could you please sit in the chair?" Dr. Beckett motions towards the chair closest to him.

Sheppard takes a step forward, but Beckett holds up a hand to stop him.

"Not you Major. Dr. Weir?"

John turns to Weir with a look of total confusion on his face. Elizabeth's only displays exasperation. She runs a hand tiredly over her face.

"Dr. Beckett..."

"Elizabeth please. Just sit in the chair."

She walks over with an exaggerated sigh and sits. The chair reacts immediately – there is a distinct hum as it comes to life. Elizabeth springs from the chair in shock.

"What the hell?!" Sheppard's outburst matches the look of total horror on Weir's face.

"Yes!" McKay exclaims. "I was right."

"What do you mean you were right? I was the one that found the second gene!"

"I meant I was right about the chairs! Why do you-"

"Both of you shut up!"

The two men fall silent at Sheppard's commanding voice. He's a little worried about Weir. She is still staring at the chair like it's going to swallow her whole. He walks over and touches her arm lightly.

"Dr. Weir?" No response. "Elizabeth? You okay?"

She turns to him, her eyes wide with shock. John gives her a little shake and hopes he doesn't end up having to slap her or anything. He has a feeling she'd slap him back in response. Luckily, there's no need to test his theory because she seems to mentally shake herself out of her stupor. She points at the chair.

"How did I do that? I shouldn't be able to do that. How the hell did I do that?!"

Weir turns to Beckett who grimaces.

"We never tested you for the ATA gene back on Earth."

"But you had my blood sample."

"Well, it turns out that we never tested it for the gene."

"Why not?"

"We started screening the team for any long term health defects before I discovered the gene. Turns out we never went back and re-tested the samples that had already been screened."

"So Dr. Weir's been able to control Ancient technology this whole time?" John asks.

"Oh it's better than that!" McKay responds, clapping his hands together with glee. "She should be able to control them as easily as you. Which means we should be able to use both of these chairs now."

"I think I need to sit down." Weir starts to sit on the command chair, realizes what she's doing, and walks over to sit against a desk.

Sheppard turns back to Beckett.

"If you didn't test her back on Earth, how did you know she'd be able to activate the chair?"

"Quite by accident actually. I was starting to believe that your gene sequence may contain two portions that allows you to easily interact with Ancient technology. I meant to compare your sequence against those already known to have the first ATA gene naturally, but the computer ran it against the entire team roster. Two of your genes matched Elizabeth's."

"You mean we're related or something?"

Sheppard pales and there's a groan from over by the desk.

"No. No. Nothing like that. But it could mean that your family lines may have, thousands of generations ago, began with the Ancients."

"So can we try both chairs now?" McKay asks excitedly.

Beckett and Sheppard both look over at Weir who is sitting with her head in her hands.

"I don't think that now is a good time, Rodney." Beckett starts to steer McKay out of the room. "We need give Dr. Weir some time to process this new information."

McKay's protests can be heard out in the hall as Sheppard walks over to Weir.

"You okay?"

"I so do not have the mental capacity for this right now." She responds without lifting her head.

"Then lets get you to bed. This can wait until morning."

John helps Elizabeth up and steers her toward her quarters. He stops short of tucking her in, but figures that sleep won't be a problem when she flops, face down on her bed fully clothed. She's asleep before the door closes behind him.


	2. Taking Flight

_There is a lot of background in this chapter, so please forgive me if it reads a little slow._

**Flying Lessons, Chapter 2**

John walks back into Elizabeth's quarters the next morning and finds her in virtually the same position that he left her in last night. She's still wearing her uniform from the day before and hasn't bothered to take off her shoes.

Elizabeth stirs when he sits on the edge of her bed. She turns toward him, but buries her head under the pillow with a groan when she sees him wearing running clothes.

"No you don't." He pulls the pillow off her head. "Come on, Legs. Get your ass up."

"Unh-uh. Don't wanna." Her arms have come up to replace the pillow and she is trying to dig her face into the mattress. He wonders how she's managing to breathe – better to be safe than sorry.

John grins and pokes his fingers in the spot just above her hip. This causes Elizabeth to squeal and jump up to a sitting position. The glare she gives him would be deadly if she wasn't so rumpled.

"Come on. You've been asleep since 17:00 yesterday. That's plenty. Go get dressed before most of Atlantis gets up."

Elizabeth grumbles something unintelligible, but gets up and goes to the bathroom attached to her quarters. She's out in a few minutes wearing her running clothes with her face freshly washed and hair slightly damp. They walk out of her quarters together and start their usual route down to and through the lower levels of Atlantis.

Their runs have become a bit of a ritual whenever she doesn't have early briefings and he's not off-world. Being at the top of Atlantis Command gives them access to all of the sleeping quarters. This makes it easy for one to help provide motivation to the other if it's needed. If anyone else in Atlantis finds it strange to see them walking in or out of each others' quarters in the early morning hours, nobody has approached them about it.

It had taken Beckett a few weeks to clear her to run again after her emergency surgery. Sheppard was waiting for her that first morning. She had quirked one eyebrow, shrugged, and started to run. He followed.

It was on that first morning, their first run together, that he had come up with his nickname for her. Elizabeth was fresh out of her recovery, so even a short run had made her very winded. John had claimed, between loud guffaws, that there was no way he could call her "Elizabeth" or "Dr. Weir" when she was dripping with sweat and panting like a dog. Deciding on the spot that none of the standard nicknames associated with Elizabeth fit her, he started calling her "Legs". She had been too busy trying to get enough oxygen in her lungs to protest. He never uses it in front of other people because he assumes, correctly, that he would then be forced to stop using it all together.

By unspoken agreement, they run in silence, using the time for inner reflection even though the company is appreciated. She has laughingly called it being alone together. Their conversations don't start until they've come to a stop on one of the balconies to catch their breath and stretch. It's very rare for these discussions to center around work. They usually talk about random things like their childhoods or old TV shows or to gossip over the constant merry-go-round of dating in Atlantis.

They have slipped into an easy friendship since their day at the island. She still works too hard and he does everything he can not to take anything too seriously. He continues to flirt outrageously with all the women he meets both in Atlantis (which she is sometimes witness to) and off-world (which he knows that Ford or McKay love to tell her about). Elizabeth teases him about it, sometimes calling him "Kirk" and he figures that is slightly better than "man-slut" – that is what she calls the character when they watch one of the many Star Trek episodes that have been downloaded into the main computer.

Elizabeth tells him that he won't ever stop. That he'll be picking up on his grandsons' dates when he's old and gray. John knows she's probably right. There's something about the start of the chase that he has always enjoyed. It's like taking off in a new experimental plane – while the entire flight is exciting, it's the take-off that leaves your heart pumping.

Elizabeth doesn't know that he never follows through with all flirting. John doesn't tell her that he pictures his grandsons looking like him, but imagines them speaking 6 or 7 languages - including Ancient. That thought should really freak him out, but it doesn't. And he's not the type of guy to over analyze stuff like that.

At the end of their run this morning, he is fairly sure he knows what she'll want to talk about. He waits until she's ready.

"Last night wasn't a dream, was it?"

"Nope."

"That's what I was afraid of."

"Why does the chair freak you out so much? It's actually pretty cool."

"I've seen the destruction that O'Neill was able to accomplish by sitting in a chair like that. Just it's existence scares the hell out of me. The fact that I may be able to control it isn't something I can put into words."

"But it's a defensive weapon."

"It's still a weapon."

"A weapon meant to protect the city."

"A weapon that almost blew you out of the sky not so long ago."

"Well...yeah..."

He didn't have a good answer for that. Even a defensive weapon is dependent on who wields it. Beckett could have killed him and General O'Neill. But if there is anyone on Atlantis he trusts more than himself with this weapon, it's Elizabeth.

"You've been worried about how we'll defend Atlantis against a Wraith attack. Now we probably can."

"I just never thought I'd be the one directly responsible for that defense."

"Well, I never thought that I'd be in another galaxy fighting soul sucking vampire things either."

"So you're telling me to suck it up and stop complaining."

"Pretty much."

Elizabeth sighs and rubs her hand over her face. She still looks tired.

"Look." It's time for him to try a different tactic. "There's more to having the Ancient gene than sitting in the chair. I'll show you."

John stands and holds his hand out to her. She hesitates for a second, then lets him help her up. Once she's standing, she narrows her eyes at him suspiciously.

"You're not going to make me wear a shield so you can shoot me, will you?"

He laughs. "No. And I'm not going to throw you off a balcony either."

"Promise?"

"Promise."

John leads them out and through the hallways of Atlantis. When he doesn't take a left at the proper corridor to their quarters, she looks up at him questioningly.

"We're not even going to get cleaned up?"

"Nope."

"Okay."

Elizabeth continues to follow him, but comes to a stop at the door into the Jumper bay.

"John..."

He gives her a grin and motions his head towards Jumper 3.

"Come on."

She doesn't move, so he walks over and grabs her by the elbow. He pulls her into the bay and toward the Jumper.

"John..."

"Don't John me, Legs. I know you've got a secret desire to be a Top Gun."

John corrals Elizabeth into the Jumper as the doors above them open to show beautiful sky. He puts her into the pilot's seat and places her hands on the controls. The ship comes to life instantly. She looks over at him with wide eyes.

"Are you really going to make me do this?"

"Oh yeah."

He settles into the other seat and flashes her another grin.

"Let's get going."

John watches Elizabeth close her eyes and take a deep a breath. He sees the look of determination when it takes over her features. She gives him one final look and he nods. The Jumper slowly rises into the air. Elizabeth swallows when she sees the city and the water below them.

"Okay. Now nice and easy. Relax and just think of where you want it to go."

This isn't the first time John has taught someone to fly a jumper. If McKay could learn, then so could Elizabeth. She takes another breath as the craft starts out over the water. They accelerate slowly as Elizabeth gets the hang of controlling the Jumper.

"Let's lose a little altitude."

The jumper drops smoothly towards the water.

"Okay. How about a turn?"

Elizabeth executes a perfect right turn and the motion pushes John into the side of his seat. He realizes just how fast they are moving over the water. He looks over and she flashes him a grin.

"Let me guess, you were a lead foot back on Earth too?"

"More tickets than I care to talk about, thank you."

He leans back with his arms behind his head and laughs.

"So...where are we headed?"

The display appears in front him, making his smile broaden. The flight plan goes out away from Atlantis and seems to stop over empty water. But he knows that area isn't empty. He is just starting to think that this is going to be a great morning, when a voice comes out over the radio.

"Major Sheppard. This is Atlantis command."

"This is Sheppard," He responds with a sigh.

"We cannot seem to locate Dr. Weir."

"I'm here Peter." John is hoping he's not imagining the sound of disappointment in her own voice.

"Dr. Weir - Sgt. Bates and his team are back. They seem eager to report."

Elizabeth raises an eyebrow at John and he shrugs. He doesn't think he could ever use the word "eager" to describe the usually over-stoic Sgt. Bates.

"Okay Peter. Major Sheppard and I are heading back now. Please tell Sgt. Hughes and his team to report to the infirmary. Briefing in a half an hour."

They weren't too far from Atlantis, so John knew that Elizabeth was giving them time to get cleaned up before the briefing.

"So. How fast do you think you can get us back?"

Sheppard immediately regrets his challenge when he's thrown into the back of his seat. Only Elizabeth's peal of laughter next to him softens the blow.


	3. Exploring

**Flying Lessons, Chapter 3**

"No signs of other humans or Wraith?"

"None, ma'am."

Elizabeth is sitting in the conference room with Sgt. Bates, Major Sheppard, and their teams. In front of them, on the table, is a stone tablet carved with Ancient writing. Bates had found some ruins on a planet called Calla and reported back to make sure he was right about the carvings being Ancient.

"Teyla, what do you know about this planet?" asks Elizabeth.

"I have never visited it myself, but I remember my father's father speaking of its people." Teyla looks sad as she continues. "However it is possible that they were wiped out in the last culling. We have not had contact with them in several generations because the Callans were not interested in trade."

The room is quiet as Elizabeth thinks. The tablet is definitely in Ancient, but there's so little decipherable text that it's difficult to make any sense of it. Bates and his team were on the planet for almost 3 days and made no contact with anything hostile or otherwise. Everything is pointing at an easy mission to learn more about the ruins and maybe find a ZPM. But something about this isn't sitting right with her. Nothing has been easy on this expedition.

She looks up at Sheppard who doesn't look too sure of this himself. When he speaks up, his thoughts seem to mirror her own.

"Don't look a gift horse in the mouth?"

Elizabeth rolls her eyes. She swears that John continues to use these kind of sayings just to see how people try and explain them to Teyla. Before Teyla can ask, Elizabeth turns to McKay.

"You've been working on a way to sweep a large area for a ZPM?"

"Yeah," McKay responds. "Peter and I have been working with one of the jumper handheld trackers and the ZPMs we have here."

"How soon will it be ready?"

"Uh...end of the day?"

"Okay." Elizabeth places her hands on table and looks at the two team leads. "Major Sheppard, Sgt. Bates. Your teams have a go to return to Calla once Dr. McKay completes the ZPM tracker. Be ready to go at 07:00 tomorrow."

She stands and everyone else follows suit. The teams start to file out of the conference room and she tries not to laugh when she hears Teyla ask Ford what a gift horse is. Elizabeth isn't too surprised when John doesn't follow the rest out of the room.

"You don't like the feel of this, do you?"

"No." She responds. "It seems too easy."

"Maybe we're due an easy mission."

"Maybe." She doesn't add that he's usually on the receiving end of bad luck when things move south of easy on these missions.

"So." One corner of his mouth lifts in a smile that's full of mischief. "You ready to try out the chairs?"

"Won't McKay want to be a witness to the first try?"

"Eh." Sheppard shrugs. "He's busy."

Elizabeth bites her lip, then nods. "Okay."

The two of them walk down to the chair room and it takes all of her willpower not to stop just outside the doors.

"Um...you first." Elizabeth allows John to choose a chair.

He sits in the left hand chair. It powers up in response to his presence. She walks up to the remaining chair, takes a deep breath, and sits. The chair responds as quickly as Sheppard's. A 3d image of Atlantis appears above them. Elizabeth can't help but appreciate the power she feels at her fingertips.

_Wow._

_Pretty cool._

_Uh...did I say that out loud?_

_Now that you mention it, no._

_You can hear what I'm thinking?_

_Way cool._

_Let's focus, shall we?_ She could feel him trying to probe deeper into her thoughts.

_You're no fun. _

_It's amazing how you can pout with just your thoughts._

_Come on, let me ask you a question._

_No._

_What? Afraid of what you'll think?_

_Focus, Major._

_Fine._

_Let's see if we can find this defensive weapon of yours._

As she thinks it, several areas on the image in front of them are highlighted in an orange-red. A grid is displayed around the outside of Atlantis.

_I don't think this chair can control them._

_Let me try._

At Sheppard's thoughts, the previously highlighted areas start to glow green and blink.

_Okay, so my chair controls the weapon. What does yours do?_

Weir focuses her thoughts on a portion of the grid around Atlantis and a small square also starts to glow green.

_Oh. It must be some sort of pin-point shield. Anything you might miss..._

_You can block. Very cool._

_I wonder what else the chairs can control._

John and Elizabeth spend another hour or so exploring Atlantis from the command chairs. They find that they can control the entire city from these chairs, including a type of close circuit video system which covers most of the main areas. Much to John's disappointment, Weir's fairly equal control of the Ancient technology means she can override some of his commands. So when they find two Atlantis team members in a compromising position in one of the more secluded public areas, she is able to quickly steer them away.

_Hey!_

_No John._

_I just wanted to see who that was._

_No John._

_I bet I could figure it out._

_You know all the women that well, do you?_

_No...but there are always distinguishing features._

_I'm sure. _

_For one, her legs aren't nearly as long as yours. _

_Let's go look at the medical area._

Elizabeth knew she's blushing. John had this amazing ability to say things in a way that would make her blush. She glances to her left and catches him looking at her. At his wink, she focuses her thoughts on Beckett's infirmary.

The video shows Beckett standing next to one of the infirmary beds. It looks like he's treating an arm burn on the patient sitting on the bed. The bed is pushed up against the wall, in front of a blank panel. They found the beds like this when they arrived in Atlantis, but have never gotten them working.

_I've always wondered what those...oops!_

Sheppard's thought activates the panel behind Beckett's patient. Weir cringes when Beckett drops the basin and syringe he was using to clean the wound. Kevin Mason, the patient sitting on the bed, tries to move, lets out a yelp of pain when he puts pressure on his arm, and nearly falls off the bed onto Beckett. Elizabeth speaks up before any more damage can be done.

"Weir to Dr. Beckett."

"Elizabeth! My God. You won't believe..."

"I know Carson. Major Sheppard apologizes for startling you." She looks pointedly at the man in the other chair.

"Sheppard?"

"Yes. We were able to start them up using the command chairs."

"Are you keeping them operational now?"

Sheppard shakes his head.

"No. They probably just needed to be activated for use."

The panel behind the bed now seems to be displaying Mason's vitals. His heartbeat has come back down to normal levels after that little scare. Beckett looks up and around assuming, correctly, that they are somehow able to see into the infirmary.

"I guess no harm done."

"Thanks Carson. Weir out."

Sheppard sit up and Weir follows suit. They look at each other and start laughing.

"Beckett looked like he was going to have a heart attack." Weir says as she wipes a tear from the corner of her eye.

"Mason just about jumped into his arms. Classic!"

"That's probably enough damage for now."

Elizabeth swings her legs to the side of the chair to stand, but has to catch herself when her legs buckle underneath her.

"Hey are you – whoa!"

John's legs have also gone out from under him. They are barely standing, using the chairs for support.

"Apparently long term use of the chairs is not good idea."

"Uh-huh."

Both of them are extremely tired. It takes a few minutes before they feel strong enough to try walking out of the room.

"I feel like I've just run a marathon."

"Or been hit by a truck."

They walk slowly down the hallways wishing they could just go to bed and get some sleep. But they have responsibilities, so they separate at one intersection - Weir to check on Beckett and Sheppard to check on McKay.

Elizabeth isn't forced to stay awake too long because Dr. Beckett immediately notices her lack of energy. He orders her to her quarters while shaking his head at what he considers foolish experimentation. Sheppard lasts less than an hour and drags himself to his own quarters before he could fall asleep in McKay's lab.

The next morning, Elizabeth still finds herself extremely tired. But even her fatigue can't suppress the dread she feels watching the two teams walk through the Stargate. John gives her a cocky smile and a sloppy salute as he walks into the event horizon. If anything, that makes the knot in the pit of her stomach tighter.

She sits through her morning briefings still unable to throw off the black cloud hanging over her. When Peter's voice rings out a mere 4 hours after the teams left Atlantis, the fear which grips her is almost paralyzing.

"Unscheduled off-world activation!"


	4. Into the Light

**Flying Lessons, Chapter 4**

"Bates IDC."

"Drop the shield."

Elizabeth just manages to keep the ice cold fear out of her voice. She does pale and Peter, who notices, starts to put the pieces together as to what is probably about to come through the gate.

"Dr. Beckett to the gate room. Possible medical emergency."

Elizabeth turns and gives Peter a small, taut smile of thanks for his quick thinking. The whole command center is silent as they wait for the first person to appear through the event horizon.

Two men walk through first, carrying a body between them. A woman runs after them, carrying two P90s. The remaining four walk through backwards, their guns pointed toward the enemy on the other side of the wormhole. The wormhole disengages and the four men lower their weapons.

Weir is running down the stairs as Ford and McKay set Sheppard down on the gateroom floor. She sees him clutching at his chest and writhing in pain. McKay, Ford, and Teyla all have blood on the front of their uniforms.

"Just hold on, sir. We're here. We're back." The total panic in Aiden's voice does nothing to reassure her or John.

Beckett's team arrives and rushes to Sheppard who is now groaning with pain through gritted teeth. Teyla has the presence of mind to stop Elizabeth before she can drop down on the floor next to John.

"You must let them work. There is nothing we can do for him."

Teyla's voice is eerily calm and Elizabeth uses its strength to pull herself together. Ford is trying to help, but is only getting in the way. McKay has to physically pull him away from their fallen commander. They run out after the medical team as they move Sheppard to the infirmary.

Weir stands just inside the infirmary doors, unintentionally staking out the same spot that Sheppard had claimed several months before. She notices, in a kind of hysterical subconscious thought, that blood from where Teyla grabbed her arm is starting to dry. She thinks that the stain will never come out now and almost laughs at the absurdity of it all.

"Aaargh!"

"Hold him down, damn it!"

Beckett and his medical team are struggling with Sheppard's flailing limbs on the bed. The doctor looks over at the people assembled at the door and whispers something to one of his staff. He squares his shoulders before walking over to Weir and Sheppard's team. One look at Carson's face tells Elizabeth that her fears are well-founded.

"No."

The word comes out in a strangled sob as the dam on her emotions breaks. Tears course, unheeded, down her cheeks and she doubles over. Only McKay's quick arm around her waist keeps her from collapsing on the floor. He's been waiting for her to crumble. Waiting for her to realize what he and Teyla knew the moment they saw the Major after he'd been shot. Nobody, not even the great John Sheppard, takes that much damage and survives.

Weir is leaning against McKay, who looks like he's trying to hold his own tears back. Teyla seems to be saying a prayer as she lets silent tears fall. Ford looks confused at Elizabeth's reaction. Beckett feels his own sadness weighing down on his shoulders as he approaches the group.

Elizabeth straightens, lifts her chin, and pulls a little way away from Rodney. She can't keep the tears from continuing to fall, but she knows that weakness is not what they need from her right now.

"Dr. Beckett?"

"Dr. Weir...I'm sorry. There's nothing to be done. The damage is too extensive. All we can do now is try to control his suffering."

"You can't just give up on him!" Beckett seems to expect Ford's outburst and shakes his head. The Lieutenant looks around frantically, not wanting to believe the look of loss already on their faces. Teyla places a hand on Aiden's arm, but a yell from over by the bed keeps her from saying anything to comfort him.

"Dr. Beckett! He won't – let us – sedate – oomph!"

Sheppard continues to struggle on the bed. He has managed to pull the IV bag down, throw a syringe across the room, and shove two nurses into the next bed. The total panic in his eyes makes Elizabeth want to run away and pretend none of this is happening. Instead, she takes slow, measured steps towards the bed.

John's thrashing stops when he sees her standing over him. Elizabeth is afraid of what her face can't hide from him. What she sees in his eyes has her leaning against the bed for support. He knows. He's not writhing in pain - he's fighting to say goodbye without medication. She motions for the nurse to move away from the bed.

His arm comes up to brush his knuckles against her cheek. Elizabeth clutches at his hand with both of her own. Her hot tears mix with the dried blood on his hand.

"Please don't leave me," she whispers. The soft smile he gives her is tragic and pierces her through the heart.

John's attention shifts away from her as the members of his team come up to say their last goodbyes. He smiles bravely for them, but the hand she holds is clenched in pain. Elizabeth looks up at the nurse holding the syringe and nods. His hand relaxes in her grip as the fast-acting sedative takes hold. His eyes rove over her face longingly one last time before they close in sleep.

Elizabeth lowers his hand to the bed and takes a step back. He's no longer in pain, which is only a small consolation. His pain is now radiating from his closest friends standing vigil at his bedside. They can do nothing but watch as the man, whose strength they've come to rely on, is taken away from them.

Elizabeth stands stiffly by the bed, her face stoic. Inside, she is railing at whatever gods rule this galaxy and how they can be so cruel. How can they take this man away from her? He has become so much more than her best friend and confidant. He's her sanity and she refuses to imagine a life without him. With the anger comes guilt. Guilt and pain over what could have been.

As she stands, watching the panel display his ever weakening heartbeat, her fury threatens to overcome her.

"No. Not today. Not like this."

Everyone in the infirmary is startled by the vehemence in Elizabeth's voice. She turns away from the bed.

"Rodney, come with me."

"But..." McKay doesn't see why she would want to be anywhere but here.

"Now."

Her tone of voice leaves no room for questions and McKay follows Weir out of the infirmary. The others watch her walk out the door and think that she's overcome with grief. Teyla knows better. She saw something flash in Weir's eyes before she left. Teyla starts to pray in earnest. Whatever Elizabeth is planning on doing, Teyla hopes she does it quickly.

Several levels down, Weir strides into the chair room and points McKay at the left hand chair.

"Sit."

"But..."

"Stop arguing with me Rodney. Sit! Just concentrate on keeping the chair active and don't get in the way."

McKay quickly sits in the command chair and Weir follows suit. She hopes she can do this on her own without Sheppard sitting in the other chair. Elizabeth takes a deep breath and an image of the infirmary appears above them.

Several people are still standing around Sheppard's bed. Teyla is holding his left hand, Ford his right. Beckett is at the foot of the bed. The sheet covering John is stained with blood and the heart monitor is beeping achingly slow.

_Please let me be right about this. I read all the reports. The Ancients were the more advanced race. If the Goa'uld and the Asgard have the technology, then surely the Ancients..._

Rodney turns in shock toward Elizabeth's chair.

"Holy crap! Why didn't I think of that?!"

_Shush Rodney, I need to concentrate._

McKay looks back at the image in front of him.

In the infirmary, a blue light starts to emanate from the ceiling above Sheppard's bed. Everyone takes a step back in shock. Teyla looks up at the light and smiles.

From her chair, Elizabeth can feel the last bit of life leaving John's body. The heart monitor in the infirmary beeps once and then stills.

_No..._

The light above the bed starts to glow a deeper blue as Elizabeth focuses all of her thought and energy into healing the man on the bed. Beneath the sheet, the torn and jagged pieces of tissue start to knit together. Elizabeth can feel her own energy draining.

_Just a little more time._

The heart monitor starts to beep in an erratic and then steady rhythm. Sheppard pulls in a ragged breath as his eyes open. His thoughts fly across to the command chair.

_Elizabeth_

_John_

The light above the bed disappears as both command chairs power down. McKay jumps up with a whoop of joy and turns toward Elizabeth.

In the infirmary, everyone rushes over to the now awake and alert Major Sheppard. He sits up and the sheet falls away, revealing smooth, undamaged skin. There is a chorus of gasps around the bed. Before anyone can verbalize their amazement, another voice sounds over the main communications system.

"McKay to Beckett. I need a little help here."


	5. Epilogue

**Flying Lesson, Epilogue**

"Do none of you understand what I mean when I say the woman needs to rest?"

Elizabeth looks over and smiles as Dr. Beckett walks into the infirmary. She is once again under strict orders to rest. Although she doesn't understand how much more rest she can get after being asleep for nearly 3 days. Her visitors agree and are eager to fill her in on the past few days.

She is sitting up with John lounging at the foot of her bed. Teyla, Aiden, and Rodney are sitting next to the bed in chairs they stole from the lab area.

"Like I was saying." Rodney ignores Beckett and continues with his explanation. "We think that the chairs are partially powered by the person sitting in them. We don't know if the Ancients had higher levels of bioelectricity or if the chairs can sense that our remaining ZPMs are low on power. Either way, you were pretty much drained like a battery."

"Almost over-drained, I might add."

Elizabeth tries not to roll her eyes at Beckett's remark. Ford's next question saves Elizabeth from yet another admonishment from the good Dr. Beckett.

"I still don't get how Dr. Weir was able to use the chair without Major Sheppard."

"Grodin thinks that it may have something to do with wrestling for control. Whenever we've tried using the chairs before, we had two people trying to make commands. If the two people have enough control over the technology, then they can work together. If not, then the chairs don't receive the proper signals. I pretty much surrendered control to Elizabeth, so she could take command without my getting in the way."

Teyla looks up at Elizabeth. "How did you know it would work?"

"I didn't." She looks across the bed at John. "But I didn't have much choice but to try."

Sheppard's mouth curves in a cocky half-smile.

"I'm grateful." He turns to McKay. "And I thank you for sitting there like a huge Energizer Bunny."

"Hey!"

Ford laughs at McKay's indignation while he slaps him on the shoulder. Teyla, once again, looks confused.

"Well I guess it's about time we found some use for Rodney."

At Beckett's comment, they all burst out laughing. It feels nice to be happy again.

"I can see that my genius isn't appreciated here. I'm going to get something to eat." McKay storms out of the infirmary in a huff. Their laughter follows him out the door.

Ford gets up to go after him. "I'll make sure that he isn't really upset."

"I'll go with you." Teyla stands, but turns toward Elizabeth first. "It is good to see you up and awake Dr. Weir."

"Same here."

"Thank you Teyla, Aiden."

The two walk out of the infirmary at which Beckett turns to look pointedly at Sheppard. He responds with a look of pure innocence.

"What?"

"Ten minutes and then you let her rest or else she's here another day." That elicits an indignant cry from Elizabeth. "And no kidnapping my patient this time."

Sheppard turns and gives Elizabeth his standard cocky grin. He wiggles his eyebrows and motions toward the door with his head when Beckett is no longer in view.

"No. I'm not staying here another day."

"Party pooper."

John gets up to lean against the bed next to Elizabeth. He starts to play with the fingers on her hand that's resting on the mattress. Elizabeth knows that he's trying to figure out what to say. She decides to make it easy for him.

"You're welcome. I'd do it again."

"That's what I'm afraid of."

She squeezes his fingers.

"Don't worry. I don't have a death wish like some people I know."

"Beckett says I'm two of nine and that he'd kill me himself if I actually tried for the remaining seven."

"I bet that was a hard one to explain to Teyla."

"A full half hour and I think she was just humoring us in the end."

They laugh a little and neither of them realize that they're still holding hands.

"Did you guys ever figure out who shot you?"

"For now, we're assuming that it was the Callans trying to protect the ruins."

"Do we know how they got a hold of a weapon that causes damage like a Goa'uld staff weapon?"

"No. I've pretty much been keeping Bates from going back and forcing the answer out of them. But you're free to give them the go ahead once you're out of here."

"I think we'll wait until we find a way to modify the vests against those weapons first."

"Figured you'd say that."

"Do you think that McKay is right? That the ZPMs we have don't have enough power to launch the defensive weapons and shield?"

"As annoying as he is, he's usually right about that kind of thing."

"So you still have your day job."

"But next time, I'll learn to listen to your woman's intuition."

"And duck when someone is shooting at you."

"That too."

John moves his hand and brushes his knuckles across Elizabeth's cheek. She leans against his hand for a moment before he drops his hand and she sits back against the pillows. They give each other shy smiles as he steps back to walk out of the infirmary.

"I'll see you tomorrow."

"Good night."

John leaves and Elizabeth lays down on the bed. As she snuggles deeper into her pillows, she can only wonder how things will change after the events of the past few days. Her last thought is that it can only get better from here.

The End.

_I hope the epilogue explains some of the questions that were floating around in the reviews. Yes, the bioelectricity bit is kind of borrowed from a certain movie, but it was the only semi-scientific thing I could think of. I'm assuming that, since Atlantis is still operational, that they have ZPMs that are just low on power. _

_This storyline is going way into the AU realm and I'm not sure how much I'm going to fight it. I have a story in mind that tackles the whole Simon issue, but I want to wait to see what happens in the upcoming episode "Home." Anywhoo...hope you like this one and there is definitely more to come._


End file.
